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Yorodumi- PDB-1q0e: Atomic resolution (1.15 ) crystal structure of bovine copper, zin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1q0e | ||||||
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Title | Atomic resolution (1.15 ) crystal structure of bovine copper, zinc superoxide dismutase | ||||||
Components | Superoxide dismutase [Cu-Zn] | ||||||
Keywords | OXIDOREDUCTASE / METAL BINDING PROTEIN / bovine / superoxide dismutase / atomic resolution / copper / zinc | ||||||
Function / homology | Function and homology information neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity ...neurofilament cytoskeleton organization / protein phosphatase 2B binding / relaxation of vascular associated smooth muscle / response to superoxide / peripheral nervous system myelin maintenance / retina homeostasis / negative regulation of cholesterol biosynthetic process / hydrogen peroxide biosynthetic process / auditory receptor cell stereocilium organization / regulation of protein kinase activity / myeloid cell homeostasis / muscle cell cellular homeostasis / superoxide metabolic process / heart contraction / superoxide dismutase / positive regulation of catalytic activity / transmission of nerve impulse / superoxide dismutase activity / regulation of multicellular organism growth / response to axon injury / ovarian follicle development / glutathione metabolic process / reactive oxygen species metabolic process / embryo implantation / dendrite cytoplasm / removal of superoxide radicals / : / locomotory behavior / regulation of mitochondrial membrane potential / positive regulation of cytokine production / sensory perception of sound / response to hydrogen peroxide / regulation of blood pressure / peroxisome / protein polyubiquitination / ubiquitin-protein transferase activity / protein-folding chaperone binding / response to heat / cytoplasmic vesicle / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / response to ethanol / intracellular iron ion homeostasis / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / copper ion binding / neuronal cell body / protein homodimerization activity / protein-containing complex / mitochondrion / zinc ion binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.15 Å | ||||||
Authors | Hough, M.A. / Hasnain, S.S. | ||||||
Citation | Journal: Structure / Year: 2003 Title: Structure of fully reduced bovine copper zinc superoxide dismutase at 1.15 A. Authors: Hough, M.A. / Hasnain, S.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1q0e.cif.gz | 148.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1q0e.ent.gz | 115.4 KB | Display | PDB format |
PDBx/mmJSON format | 1q0e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q0/1q0e ftp://data.pdbj.org/pub/pdb/validation_reports/q0/1q0e | HTTPS FTP |
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-Related structure data
Related structure data | 1cbjS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15599.375 Da / Num. of mol.: 2 / Fragment: Copper, Zinc Superoxide Dismutase / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Cell: erythrocyte / References: UniProt: P00442, superoxide dismutase #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 15 % PEG-4000, 50 mM glycyl-glycine , 100 mM NaCl, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 1, 2001 |
Radiation | Monochromator: Daresbury / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87 Å / Relative weight: 1 |
Reflection | Resolution: 1.15→75 Å / Num. all: 119010 / Num. obs: 119010 / % possible obs: 94.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.078 |
Reflection shell | Resolution: 1.15→1.18 Å / % possible all: 71.1 |
-Processing
Software |
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Refinement | Method to determine structure: AB INITIO Starting model: 1CBJ Resolution: 1.15→50 Å / Num. parameters: 24333 / Num. restraintsaints: 28796 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
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Refine analyze | Num. disordered residues: 13 / Occupancy sum hydrogen: 2114 / Occupancy sum non hydrogen: 2668.24 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.15→50 Å
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Refine LS restraints |
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